How to interface with TCGA https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html https://bioconductor.org/packages/release/workflows/vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.html#Environment

Loading the annotation file:

data("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
anno <- getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
load("/Users/adiallo/Desktop/Dartmouth/Christiansen_lab/CF_Project/Methylation/Annotation/EPIC.hg19.manifest.RDATA")
attach(annotation)
manifest <- getManifest(IlluminaHumanMethylationEPICmanifest)

Loading the data and metadata information

targets <- read.csv("/Users/adiallo/Desktop/Thesis/Data_Documents/dm_57_samples.csv")
targets$patient <- paste(targets$Sentrix_ID,targets$Sentrix_Position,sep="_")
rownames(targets) <- targets$patient
targets$SampleID<- targets$patient

targets_expanded <- read.csv("/Users/adiallo/Desktop/Thesis/Data_Documents/data_all.csv")
targets_expanded$patient <- paste(targets$Sentrix_ID,targets$Sentrix_Position,sep="_")
rownames(targets_expanded) <- targets_expanded$patient
targets_expanded$SampleID<- targets_expanded$patient
targets = targets_expanded
idat = "/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/no_match/"
RGset_32 = read.metharray.exp("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/no_match/idats/",recursive = TRUE) 
#RGset_25 = openSesame(idat , func = getBetas) 
RGset_25 = read.metharray.exp("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/no_match/25_samples/",recursive = TRUE) 

Get GTEx data


Betas_GTEx = readRDS("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/GTEx/GTEx_samples.rds")
targets_GTEx <- read.csv("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/GTEx/targets.csv")
targets_GTEx$patient <- targets_GTEx$Filename
rownames(targets_GTEx) <- targets_GTEx$patient
targets_GTEx$SampleID<- targets_GTEx$patient

Get TCGA data

tcga.data <- readRDS("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/TCGA/TCGA_data.rds")
tcga.dnam <- tcga.data[["dnam"]]
tcga.pheno <- tcga.data[["pheno"]]
tcga.cell <- tcga.data[["cell_types"]]
msi_dat<-readRDS("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/TCGA/msi_tcga.rds")
tcga.cell$COAD_Deconv1#$MSS
tcga.cell$COAD_Deconv2#MASS

tcga_T = t(tcga.dnam)

# MSet_noob_T <- preprocessNoob(tcga.dnam)
# beta_matrix_TCGA<-getBeta(MSet_noob_T)

For obtaining more data


files <- getResults(query.met)
head(files$file_id)
[1] "9d067dc1-0dc1-412e-a647-b9203ca503da" "fc14a20c-7c24-4235-8fad-f802355771bc" "8b09dddb-b19e-4ba7-ad11-c634053f9c23"
[4] "49b26be9-b1f8-4f14-8e78-ac5db2ba0d59" "656ae34a-599c-4c0e-83d0-8a3225996e55" "b933669d-424e-4bc4-92f9-467687c28c73"
LS0tCnRpdGxlOiAiVGVzdGluZyBDb250cm9scyIKb3V0cHV0OiBodG1sX25vdGVib29rCi0tLQoKSG93IHRvIGludGVyZmFjZSB3aXRoIFRDR0EKaHR0cHM6Ly9iaW9jb25kdWN0b3Iub3JnL3BhY2thZ2VzL2RldmVsL2Jpb2MvdmlnbmV0dGVzL1RDR0FiaW9saW5rcy9pbnN0L2RvYy9pbmRleC5odG1sCmh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy9yZWxlYXNlL3dvcmtmbG93cy92aWduZXR0ZXMvVENHQVdvcmtmbG93L2luc3QvZG9jL1RDR0FXb3JrZmxvdy5odG1sI0Vudmlyb25tZW50CgpgYGB7ciBtZXNzYWdlPUZBTFNFLCB3YXJuaW5nPUZBTFNFLCBpbmNsdWRlPUZBTFNFfQpsaWJyYXJ5KG1pbmZpKQpsaWJyYXJ5KHNlc2FtZSkKbGlicmFyeShwaGVhdG1hcCkKbGlicmFyeShtaW5maURhdGEpCmxpYnJhcnkoRmxvd1NvcnRlZC5CbG9vZC5FUElDKQpsaWJyYXJ5KEhpVElNRUQpCmxpYnJhcnkoZ2dwbG90MikKbGlicmFyeShJbGx1bWluYUh1bWFuTWV0aHlsYXRpb25FUElDYW5uby5pbG0xMGI0LmhnMTkpCmxpYnJhcnkoSWxsdW1pbmFIdW1hbk1ldGh5bGF0aW9uRVBJQ3YybWFuaWZlc3QpCmxpYnJhcnkoSWxsdW1pbmFIdW1hbk1ldGh5bGF0aW9uRVBJQ3YyYW5uby4yMGExLmhnMzgpCmxpYnJhcnkoSWxsdW1pbmFIdW1hbk1ldGh5bGF0aW9uRVBJQ21hbmlmZXN0KQpsaWJyYXJ5KGxpbW1hKQpsaWJyYXJ5KHF2YWx1ZSkKbGlicmFyeShzdmEpCmxpYnJhcnkoRU5taXgpCmxpYnJhcnkoZ2dwbG90MikKbGlicmFyeShnZ3JlcGVsKQpsaWJyYXJ5KG1hdHJpeFN0YXRzKQpsaWJyYXJ5KEVwaURJU0gpCmxpYnJhcnkodGliYmxlKQpsaWJyYXJ5KHRpZHlyKQpsaWJyYXJ5KGRwbHlyKQpsaWJyYXJ5KG1ldGh5bEdTQSkKYGBgCgpMb2FkaW5nIHRoZSBhbm5vdGF0aW9uIGZpbGU6CmBgYHtyfQpkYXRhKCJJbGx1bWluYUh1bWFuTWV0aHlsYXRpb25FUElDYW5uby5pbG0xMGI0LmhnMTkiKQphbm5vIDwtIGdldEFubm90YXRpb24oSWxsdW1pbmFIdW1hbk1ldGh5bGF0aW9uRVBJQ2Fubm8uaWxtMTBiNC5oZzE5KQpsb2FkKCIvVXNlcnMvYWRpYWxsby9EZXNrdG9wL0RhcnRtb3V0aC9DaHJpc3RpYW5zZW5fbGFiL0NGX1Byb2plY3QvTWV0aHlsYXRpb24vQW5ub3RhdGlvbi9FUElDLmhnMTkubWFuaWZlc3QuUkRBVEEiKQphdHRhY2goYW5ub3RhdGlvbikKbWFuaWZlc3QgPC0gZ2V0TWFuaWZlc3QoSWxsdW1pbmFIdW1hbk1ldGh5bGF0aW9uRVBJQ21hbmlmZXN0KQoKYGBgCgpMb2FkaW5nIHRoZSBkYXRhIGFuZCBtZXRhZGF0YSBpbmZvcm1hdGlvbgpgYGB7cn0KdGFyZ2V0cyA8LSByZWFkLmNzdigiL1VzZXJzL2FkaWFsbG8vRGVza3RvcC9UaGVzaXMvRGF0YV9Eb2N1bWVudHMvZG1fNTdfc2FtcGxlcy5jc3YiKQp0YXJnZXRzJHBhdGllbnQgPC0gcGFzdGUodGFyZ2V0cyRTZW50cml4X0lELHRhcmdldHMkU2VudHJpeF9Qb3NpdGlvbixzZXA9Il8iKQpyb3duYW1lcyh0YXJnZXRzKSA8LSB0YXJnZXRzJHBhdGllbnQKdGFyZ2V0cyRTYW1wbGVJRDwtIHRhcmdldHMkcGF0aWVudAoKdGFyZ2V0c19leHBhbmRlZCA8LSByZWFkLmNzdigiL1VzZXJzL2FkaWFsbG8vRGVza3RvcC9UaGVzaXMvRGF0YV9Eb2N1bWVudHMvZGF0YV9hbGwuY3N2IikKdGFyZ2V0c19leHBhbmRlZCRwYXRpZW50IDwtIHBhc3RlKHRhcmdldHMkU2VudHJpeF9JRCx0YXJnZXRzJFNlbnRyaXhfUG9zaXRpb24sc2VwPSJfIikKcm93bmFtZXModGFyZ2V0c19leHBhbmRlZCkgPC0gdGFyZ2V0c19leHBhbmRlZCRwYXRpZW50CnRhcmdldHNfZXhwYW5kZWQkU2FtcGxlSUQ8LSB0YXJnZXRzX2V4cGFuZGVkJHBhdGllbnQKdGFyZ2V0cyA9IHRhcmdldHNfZXhwYW5kZWQKYGBgCgpgYGB7cn0KaWRhdCA9ICIvVXNlcnMvYWRpYWxsby9EZXNrdG9wL1RoZXNpcy9EYXRhX0RvY3VtZW50cy9BbGxfRGF0YS9ETkFfTWV0aHlsYXRpb24vZG1fZGF0YS9ub19tYXRjaC8iClJHc2V0XzMyID0gcmVhZC5tZXRoYXJyYXkuZXhwKCIvVXNlcnMvYWRpYWxsby9EZXNrdG9wL1RoZXNpcy9EYXRhX0RvY3VtZW50cy9BbGxfRGF0YS9ETkFfTWV0aHlsYXRpb24vZG1fZGF0YS9ub19tYXRjaC9pZGF0cy8iLHJlY3Vyc2l2ZSA9IFRSVUUpIAojUkdzZXRfMjUgPSBvcGVuU2VzYW1lKGlkYXQgLCBmdW5jID0gZ2V0QmV0YXMpIApSR3NldF8yNSA9IHJlYWQubWV0aGFycmF5LmV4cCgiL1VzZXJzL2FkaWFsbG8vRGVza3RvcC9UaGVzaXMvRGF0YV9Eb2N1bWVudHMvQWxsX0RhdGEvRE5BX01ldGh5bGF0aW9uL2RtX2RhdGEvbm9fbWF0Y2gvMjVfc2FtcGxlcy8iLHJlY3Vyc2l2ZSA9IFRSVUUpIApgYGAKCkdldCBHVEV4IGRhdGEKYGBge3J9CgpCZXRhc19HVEV4ID0gcmVhZFJEUygiL1VzZXJzL2FkaWFsbG8vRGVza3RvcC9UaGVzaXMvRGF0YV9Eb2N1bWVudHMvQWxsX0RhdGEvRE5BX01ldGh5bGF0aW9uL2RtX2RhdGEvR1RFeC9HVEV4X3NhbXBsZXMucmRzIikKdGFyZ2V0c19HVEV4IDwtIHJlYWQuY3N2KCIvVXNlcnMvYWRpYWxsby9EZXNrdG9wL1RoZXNpcy9EYXRhX0RvY3VtZW50cy9BbGxfRGF0YS9ETkFfTWV0aHlsYXRpb24vZG1fZGF0YS9HVEV4L3RhcmdldHMuY3N2IikKdGFyZ2V0c19HVEV4JHBhdGllbnQgPC0gdGFyZ2V0c19HVEV4JEZpbGVuYW1lCnJvd25hbWVzKHRhcmdldHNfR1RFeCkgPC0gdGFyZ2V0c19HVEV4JHBhdGllbnQKdGFyZ2V0c19HVEV4JFNhbXBsZUlEPC0gdGFyZ2V0c19HVEV4JHBhdGllbnQKCmBgYAoKR2V0IFRDR0EgZGF0YQoKYGBge3J9CnRjZ2EuZGF0YSA8LSByZWFkUkRTKCIvVXNlcnMvYWRpYWxsby9EZXNrdG9wL1RoZXNpcy9EYXRhX0RvY3VtZW50cy9BbGxfRGF0YS9ETkFfTWV0aHlsYXRpb24vZG1fZGF0YS9UQ0dBL1RDR0FfZGF0YS5yZHMiKQp0Y2dhLmRuYW0gPC0gdGNnYS5kYXRhW1siZG5hbSJdXQp0Y2dhLnBoZW5vIDwtIHRjZ2EuZGF0YVtbInBoZW5vIl1dCnRjZ2EuY2VsbCA8LSB0Y2dhLmRhdGFbWyJjZWxsX3R5cGVzIl1dCm1zaV9kYXQ8LXJlYWRSRFMoIi9Vc2Vycy9hZGlhbGxvL0Rlc2t0b3AvVGhlc2lzL0RhdGFfRG9jdW1lbnRzL0FsbF9EYXRhL0ROQV9NZXRoeWxhdGlvbi9kbV9kYXRhL1RDR0EvbXNpX3RjZ2EucmRzIikKdGNnYS5jZWxsJENPQURfRGVjb252MSMkTVNTCnRjZ2EuY2VsbCRDT0FEX0RlY29udjIjTUFTUwoKdGNnYV9UID0gdCh0Y2dhLmRuYW0pCgojIE1TZXRfbm9vYl9UIDwtIHByZXByb2Nlc3NOb29iKHRjZ2EuZG5hbSkKIyBiZXRhX21hdHJpeF9UQ0dBPC1nZXRCZXRhKE1TZXRfbm9vYl9UKQoKYGBgCgoKCgpGb3Igb2J0YWluaW5nIG1vcmUgZGF0YQpgYGB7cn0KbGlicmFyeShUQ0dBYmlvbGlua3MpCgojIFNwZWNpZnkgdGhlIGV4YWN0IGRhdGEgdHlwZSAodXN1YWxseSBiZXRhLXZhbHVlcykKcXVlcnkubWV0IDwtIEdEQ3F1ZXJ5KAogIHByb2plY3QgPSAiVENHQS1DT0FEIiwKICBkYXRhLmNhdGVnb3J5ID0gIkROQSBNZXRoeWxhdGlvbiIsCiAgZGF0YS50eXBlID0gIk1ldGh5bGF0aW9uIEJldGEgVmFsdWUiLAogIHBsYXRmb3JtID0gIklsbHVtaW5hIEh1bWFuIE1ldGh5bGF0aW9uIDQ1MCIKKQoKZmlsZXMgPC0gZ2V0UmVzdWx0cyhxdWVyeS5tZXQpCmhlYWQoZmlsZXMkZmlsZV9pZCkKIyBEb3dubG9hZCB0aGUgZGF0YQpHRENkb3dubG9hZChxdWVyeS5tZXQpCgojIFByZXBhcmUgZGF0YSBmb3IgYW5hbHlzaXMKZGF0YS5tZXQgPC0gR0RDcHJlcGFyZShxdWVyeS5tZXQpCmBgYAoK